Contacts of the helix formed by residues 94 - 109 (chain D) in PDB entry 2P1N
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 94 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50D LYS* 5.1 2.6 + - - -
93D ILE* 1.3 80.7 - - - +
95D GLN* 1.3 75.4 + - - +
96D ALA* 2.9 19.4 + - - +
97D THR* 3.1 22.3 + - - -
98D LEU* 3.1 24.1 + - - +
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Residues in contact with GLN 95 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94D ASP* 1.3 78.2 + - - +
96D ALA* 1.3 68.5 + - - +
97D THR 2.8 3.3 + - - -
98D LEU* 3.8 6.1 - - - +
99D PHE* 3.0 54.1 + - + -
124D MET* 3.9 17.7 - - + +
136D THR* 2.6 37.3 + - - +
137D PHE* 4.3 1.0 - - - +
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Residues in contact with ALA 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D ASP* 2.9 7.8 + - - +
95D GLN* 1.3 80.8 - - - +
97D THR* 1.3 58.7 + - - +
99D PHE* 3.2 24.5 - - - +
100D GLU* 3.4 11.3 + - - +
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Residues in contact with THR 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D LYS* 3.5 33.2 + - - -
51D ILE* 4.4 9.8 - - + +
54D LYS* 5.2 9.6 - - + -
93D ILE* 3.7 17.7 - - + -
94D ASP* 3.1 26.4 + - - -
95D GLN 2.8 3.0 + - - -
96D ALA* 1.3 77.0 - - - +
98D LEU* 1.3 61.5 + - - +
100D GLU* 2.8 11.6 + - - +
101D LEU* 2.8 32.2 + - + +
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Residues in contact with LEU 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D MET* 3.5 30.1 - - + -
93D ILE* 3.0 19.4 - - + +
94D ASP 3.1 11.5 + - - +
95D GLN* 3.9 4.5 - - - +
97D THR* 1.3 78.4 - - - +
99D PHE* 1.3 69.3 + - + +
101D LEU* 3.3 6.0 - - + +
102D ILE* 2.9 25.5 + - - +
117D THR* 4.3 17.3 - - + +
120D THR* 3.9 22.2 - - + -
121D VAL* 4.2 16.4 - - + -
124D MET* 4.0 26.5 - - - -
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Residues in contact with PHE 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D GLN* 3.0 51.9 + - + -
96D ALA* 3.2 18.2 - - - +
97D THR 3.3 0.2 - - - -
98D LEU* 1.3 82.1 - - + +
100D GLU* 1.3 57.6 + - - +
102D ILE* 3.7 6.2 - - - +
103D LEU* 3.5 26.8 + - + +
121D VAL* 4.8 6.1 - - + -
124D MET* 4.2 15.5 - - + -
137D PHE* 4.1 34.1 - + + -
138D ASN 5.8 0.7 - - - -
9E PHE* 4.3 28.8 - + + -
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Residues in contact with GLU 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D THR* 3.9 19.2 + - - -
50D LYS* 5.2 4.7 - - - +
51D ILE* 3.7 29.4 - - + +
96D ALA 3.4 8.9 + - - +
97D THR* 2.8 14.1 + - - +
99D PHE* 1.3 73.0 - - - +
101D LEU* 1.3 56.4 + - - +
103D LEU* 3.1 15.5 + - + +
104D ALA* 2.8 34.7 + - - +
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Residues in contact with LEU 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D ILE* 4.2 9.1 - - + +
54D LYS* 4.3 22.2 - - + -
55D VAL* 3.9 27.8 - - + +
90D PHE* 4.0 26.5 - - + -
91D MET* 4.3 11.4 - - + -
93D ILE* 5.0 2.0 - - + -
97D THR* 2.8 18.7 + - + +
98D LEU* 3.3 14.6 - - - +
100D GLU* 1.3 71.9 - - - +
102D ILE* 1.3 67.0 + - - +
104D ALA* 3.1 4.7 + - - +
105D ALA* 2.9 25.6 + - - +
113D LEU* 4.2 8.3 - - + -
117D THR* 3.6 23.8 - - + -
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Residues in contact with ILE 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D LEU* 2.9 23.5 + - + +
99D PHE* 3.7 7.9 - - - +
101D LEU* 1.3 72.5 - - - +
103D LEU* 1.3 65.9 + - + +
105D ALA* 3.3 3.6 + - - +
106D ASN* 3.1 21.1 + - - +
114D LEU* 4.4 3.0 - - + +
117D THR* 3.5 48.6 - - - +
118D CYS* 4.0 15.3 - - - -
121D VAL* 3.7 21.8 - - + -
9E PHE* 4.3 15.7 - - + -
13E VAL* 3.5 30.7 - - + -
17E VAL* 4.6 1.1 - - + -
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Residues in contact with LEU 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D PHE* 3.5 16.8 + - + +
100D GLU* 3.1 18.8 + - + +
102D ILE* 1.3 80.9 - - + +
104D ALA* 1.3 58.2 + - - +
106D ASN* 3.3 7.5 + - - +
107D TYR* 2.9 30.8 + - - +
8E SER 4.4 13.9 - - - +
9E PHE* 4.4 8.1 - - + -
10E PRO* 3.9 31.2 - - + -
13E VAL* 5.5 0.9 - - + -
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Residues in contact with ALA 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D ASN 5.6 3.1 - - - +
47D VAL* 4.0 15.3 - - + -
51D ILE* 3.5 32.1 - - + -
55D VAL* 4.1 10.5 - - + -
100D GLU 2.8 11.4 + - - +
101D LEU 3.6 4.0 - - - +
103D LEU* 1.3 76.6 - - - +
105D ALA* 1.3 52.8 + - - +
107D TYR* 4.2 7.9 - - - -
108D LEU* 2.7 44.2 + - + +
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Residues in contact with ALA 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D LEU 2.9 13.4 + - - +
102D ILE 3.6 4.9 - - - +
103D LEU 3.3 0.2 - - - -
104D ALA* 1.3 74.9 - - - +
106D ASN* 1.3 60.4 + - - +
109D ASN* 2.9 23.2 + - - -
110D ILE* 3.1 17.4 + - - +
113D LEU* 3.3 39.2 - - + +
114D LEU* 3.8 22.9 - - - +
117D THR* 4.5 2.5 - - - +
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Residues in contact with ASN 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ILE 3.1 13.5 + - - +
103D LEU* 3.5 10.5 + - - +
105D ALA* 1.3 77.3 - - - +
107D TYR* 1.3 60.8 + - - +
109D ASN* 2.9 28.0 + - - +
114D LEU* 4.2 20.1 - - + +
10E PRO* 4.0 11.1 - - - +
12E GLU* 3.6 33.9 + - - +
13E VAL* 3.6 27.2 - - + +
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Residues in contact with TYR 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D THR* 2.5 38.6 + - + -
32D MET* 4.0 16.3 - - + +
44D LEU* 4.2 6.0 - - + +
45D PRO* 3.6 22.2 - - - +
46D ASN* 3.3 51.0 + - + -
47D VAL* 3.8 26.5 - - + -
103D LEU 2.9 17.8 + - - +
104D ALA* 3.6 5.2 - - - +
106D ASN* 1.3 80.4 - - - +
108D LEU* 1.3 57.5 + - + +
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Residues in contact with LEU 108 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26D SER* 2.4 35.2 + - - +
28D THR* 3.0 18.7 + - + -
29D ILE* 3.8 30.1 - - + -
44D LEU* 4.0 20.2 - - + -
47D VAL* 4.3 17.7 - - + -
52D LEU* 5.6 1.8 - - + -
55D VAL* 4.0 27.8 - - + -
104D ALA* 2.7 33.3 + - + +
107D TYR* 1.3 81.3 - - + +
109D ASN* 1.4 63.5 + - - +
110D ILE* 3.5 10.1 - - + -
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Residues in contact with ASN 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D GLU 3.7 2.4 - - - +
27D GLN* 3.1 44.5 + - + +
28D THR* 3.8 18.2 + - - +
31D HIS* 5.8 2.4 - - - -
105D ALA 2.9 10.1 + - - -
106D ASN* 2.9 23.1 + - - +
107D TYR 4.6 0.2 - - - +
108D LEU* 1.4 78.1 - - - +
110D ILE* 1.3 57.8 + - - +
111D LYS 3.8 2.4 + - - -
114D LEU* 6.2 2.0 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il